On Feb 7, 2013, at 2:29 PM, greg wrote:
I think I found the problem. The TMPDIR environment variable was set
to /tmp/5393732.1.f03.q for jobs galaxy was running. (I guess the
admins do this?)
SGE does this to create a job-specific temporary directory that it can clean up
after each job
Update:
When I run as the Galaxy user, Python does have the right temp directory:
tempfile.gettempdir()
'/scratch/galaxy'
So does that mean this upload job isn't running as galaxy, or is
skipping the job_environment_setup_file? Or could something else be
going on?
Any ideas, now I'm really
Could I modify /misc/local/galaxy/galaxy-dist/lib/galaxy/datatypes/sniff.py
to print out debug information like host, os.environ,
tempfile.gettempdir(), etc?
Would I be able to see its stdout from galaxy or the log, or is there
something special I need to do to retrieve the information?
On Thu,
I think I found the problem. The TMPDIR environment variable was set
to /tmp/5393732.1.f03.q for jobs galaxy was running. (I guess the
admins do this?)
I updated /usr/local/galaxy/job_environment_setup_file and also
/home/galaxy/.bashrc to set TMPDIR to /scratch/galaxy and it seems to
work now.
Hi guys,
When I try to upload a directory of files from a server directory I'm
seeing the error below.
It appears to be trying to write to a temp directory somewhere that
I'm guessing doesn't have enough space? Is there a way I can direct
where it writes to for temporary files like this?
Am I
On Feb 6, 2013, at 2:32 PM, greg wrote:
Hi guys,
When I try to upload a directory of files from a server directory I'm
seeing the error below.
It appears to be trying to write to a temp directory somewhere that
I'm guessing doesn't have enough space? Is there a way I can direct
where
Thanks Nate,
It turns out I already had this as the first line of my job setup file:
export TEMP=/scratch/galaxy
But when I look in that directory, there's plenty of free space, and I
also don't see any recent files there. So I'm wondering if the upload
jobs aren't seeing that for some reason.
On Feb 6, 2013, at 3:00 PM, greg wrote:
Thanks Nate,
It turns out I already had this as the first line of my job setup file:
export TEMP=/scratch/galaxy
But when I look in that directory, there's plenty of free space, and I
also don't see any recent files there. So I'm wondering if
Hmm, I narrowed down the problem some more:
For some reason Python isn't respecting the TEMP environment
variable so it's trying to write to /tmp on whichever node it's
running on.
I really don't understand why Python isn't respecting it. The docs
seem to suggest it should:
Ok, when I ran Python in my last two emails I was running as myself,
not the galaxy user, and only the galaxy user has write permission to
/scratch/galaxy
So that's why Python was ignoring /scratch/galaxy for me. If it
doesn't have write access it tries the next temp directory in its
list.
I'm
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